Evaluation of MALDI-TOF MS for molecular typing of Acinetobacter baumannii in comparison with orthogonal methods. Evaluation of MALDI-TOF MS for molecular typing of Acinetobacter baumannii in comparison with orthogonal methods

Colonisation and subsequent healthcare associated infection (HCAI) with Acinetobacter baumannii is a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multi drug-resistant strains are associated with increased patient morbidity, mortality and poorer overall outcomes. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks. In addition to methods deployed by reference laboratories, Matrix Assisted Laser Desorption/Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF MS) may assist by making initial in-house judgements on strain relatedness. However, limited studies on method reproducibility exist for this application. We applied MALDI-TOF MS typing to A. baumannii isolates associated with a nosocomial outbreak and evaluated different methods for data analysis. In addition, we compared MALDI-TOF MS with whole genome sequencing (WGS) and Fourier-transform infrared spectroscopy (FTIR) as orthogonal methods to further explore their resolution for bacterial strain typing. A related sub-group of isolates consistently clustered separately to the main outbreak group by all investigated methods. This finding, combined with epidemiological data from the outbreak, indicates that these methods identified a separate transmission event unrelated to the main outbreak. However, the MALDI-TOF MS upstream approach introduced measurement variability impacting upon method reproducibility and limiting its reliability as a stand-alone typing method. Emerging typing methods which offer different degrees of resolution, and target different biomolecules, could be utilised in-house to more quickly confirm or rule out transmission events. This work highlights some of the steps to be improved before such tools can be fully integrated into routine diagnostic service workflows for strain typing.

鲍曼不动杆菌（Acinetobacter baumannii）定植及其继发的医院获得性感染（healthcare associated infection, HCAI）是医院环境中脆弱患者群体的重点健康隐患。涉及多重耐药菌株的暴发疫情会升高患者的发病率与死亡率，同时拉低整体预后水平。可靠的分子分型方法可助力追踪传播路径、管控暴发疫情。除参考实验室常规采用的分型手段外，基质辅助激光解吸电离飞行时间质谱（Matrix Assisted Laser Desorption/Ionisation-Time of Flight Mass Spectrometry, MALDI-TOF MS）可通过完成初步的内部菌株相关性判断，为疫情防控提供辅助支持。但目前针对该应用场景下方法重现性的研究仍较为匮乏。
本研究将MALDI-TOF MS分型技术应用于与医院暴发相关的鲍曼不动杆菌分离株，并评估了多种数据分析方案。此外，本研究还将MALDI-TOF MS与全基因组测序（whole genome sequencing, WGS）、傅里叶变换红外光谱（Fourier-transform infrared spectroscopy, FTIR）这两种正交技术进行对比，以进一步探究三者在细菌菌株分型中的分辨能力。
研究结果显示，一组关联的分离株经所有受试方法检测，均与主要暴发组呈现聚类分离状态。结合本次暴发的流行病学数据，该发现表明这些分型方法均识别出了一起独立于主要暴发的传播事件。不过，MALDI-TOF MS的上游实验流程会引入测量变异性，这对方法重现性造成负面影响，限制了其作为独立分型方法的可靠性。
后续可将针对不同生物分子、提供不同分辨程度的新兴分型技术应用于内部实验室，以更快确认或排除传播事件。本研究凸显了在这类工具完全整合至菌株分型的常规诊断服务工作流程前，仍有诸多步骤亟待优化完善。